revdep/problems.md

In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

ACE

• Version: 1.2.0
• Source code: https://github.com/cran/ACE
• URL: https://github.com/tgac-vumc/ACE
• Date/Publication: 2019-05-02
• Number of recursive dependencies: 85

Run revdep_details(,"ACE") for more info

In both

• checking dependencies in R code ... NOTE Unexported object imported by a ':::' call: ‘QDNAseq:::sdDiffTrim’ See the note in ?`:::` about the use of this operator.

• checking Rd cross-references ... NOTE Package unavailable to check Rd xrefs: ‘corrplot’

GeneBreak

• Version: 1.14.0
• Source code: https://github.com/cran/GeneBreak
• URL: https://github.com/stefvanlieshout/GeneBreak
• Date/Publication: 2019-05-02
• Number of recursive dependencies: 33

Run revdep_details(,"GeneBreak") for more info

In both

• checking R code for possible problems ... NOTE .glmbreak: no visible global function definition for ‘glm’ .glmbreak: no visible global function definition for ‘predict’ addGeneAnnotation,CopyNumberBreakPoints: no visible global function definition for ‘head’ bpStats,CopyNumberBreakPoints: no visible global function definition for ‘sd’ bpStats,CopyNumberBreakPoints: no visible global function definition for ‘p.adjust’ Undefined global functions or variables: glm head p.adjust predict sd Consider adding importFrom("stats", "glm", "p.adjust", "predict", "sd") importFrom("utils", "head") to your NAMESPACE file.

HiCcompare

• Version: 1.6.0
• Source code: https://github.com/cran/HiCcompare
• Date/Publication: 2019-05-02
• Number of recursive dependencies: 143

Run revdep_details(,"HiCcompare") for more info

In both

• checking package dependencies ... NOTE Package suggested but not available for checking: 'multiHiCcompare'

• checking installed package size ... NOTE installed size is 6.5Mb sub-directories of 1Mb or more: data 5.6Mb

• checking R code for possible problems ... NOTE ... sim.other.methods: no visible binding for global variable ‘IF2’ sim.other.methods: no visible binding for global variable ‘adj.M’ sim.other.methods: no visible binding for global variable ‘M’ sim_matrix: no visible binding for global variable ‘bias.slope’ total_sum: no visible binding for global variable ‘IF2’ total_sum: no visible binding for global variable ‘M’ total_sum: no visible binding for global variable ‘IF1’ total_sum: no visible binding for global variable ‘chr1’ volcano: no visible binding for global variable ‘A’ volcano: no visible binding for global variable ‘adj.IF1’ volcano: no visible binding for global variable ‘adj.IF2’ volcano: no visible binding for global variable ‘p.value’ volcano: no visible binding for global variable ‘D’ Undefined global functions or variables: A D IF IF1 IF2 M Z adj.IF1 adj.IF2 adj.M axis bias.slope bp centromere_locations chr1 chr2 count fold.change i j p.adj p.value pnorm region1 region2 start1 start2 Consider adding importFrom("graphics", "axis") importFrom("stats", "D", "pnorm") to your NAMESPACE file.

QDNAseq.hg19

• Version: 1.14.0
• Source code: https://github.com/cran/QDNAseq.hg19
• URL: https://github.com/tgac-vumc/QDNAseq.hg19
• BugReports: https://github.com/tgac-vumc/QDNAseq.hg19/issues
• Date/Publication: 2019-05-07
• Number of recursive dependencies: 33

Run revdep_details(,"QDNAseq.hg19") for more info

In both

• checking installed package size ... NOTE installed size is 35.4Mb sub-directories of 1Mb or more: data 35.3Mb

QDNAseq.mm10

• Version: 1.14.0
• Source code: https://github.com/cran/QDNAseq.mm10
• URL: https://github.com/tgac-vumc/QDNAseq.mm10
• BugReports: https://github.com/tgac-vumc/QDNAseq.mm10/issues
• Date/Publication: 2019-05-07
• Number of recursive dependencies: 33

Run revdep_details(,"QDNAseq.mm10") for more info

In both

• checking installed package size ... NOTE installed size is 31.3Mb sub-directories of 1Mb or more: data 31.2Mb

ccagc/QDNAseq documentation built on July 28, 2024, 3:46 p.m.